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I am headed out the door to the 2007 International Genetically Engineered Machines (iGEM) Competition at MIT. There look to be ~56 teams composed of ~400 students from around the world. As I am a judge this year, I won't be blogging any more about it until it's over.
I have been looking forward to this for months -- it should be great fun.
I'm in Houston today, speaking to a small group of American Petroleum Institute members about the future of biofuels (Thanks for the recommendation, Jamais). More air travel in the service of explaining carbon neutral fuels. Nonetheless, the view from the 49th floor of the Shell Plaza tower is remarkable.
I am told by residents that Houston has evidently just decided the answer to local traffic and transit issues is to widen I-10 from 15 to 22 lanes. They are apparently proud of the 2 HOV lanes that will come with the expansion.
Huh.
Over the last several months I have had the opportunity to talk to a good number of oil and gas executives. Way back, say, just last summer, when oil was only at $65 per barrel, it still seemed like a stretch for the oil guys (yes, all guys) to claim oil would hit $100 by the end of 2007. Now, according to Reuters, oil has just hit $92 per barrel, up 30% since August alone. It seems the C-note per barrel may arrive quite soon.
Part of this run up in price is due to the decline of the dollar, which may further encourage a shift to trading oil in euros. The follow on effect of moving so much trade away from the dollar can't be seen as a good sign for the U.S. economy. Yes, it is still true that foreign governments still hold large amounts of U.S. government debt, which will always be denominated in dollar and which gives many nations an interest in propping up U.S. currency. But slippage in international use of the dollar for trade makes me even less interested in keeping any business I do here in the U.S. I have just accepted my first project from Canada, and the contract stipulates pay in Canadian currency. I might even ponder leaving it in that currency, as the Canadian dollar has been appreciating with respect to the U.S. dollar at a fairly decent rate.
Anyway -- back to oil -- a significant motivation in the increase in price is limitation of supply and increased demand. Some of this will get fixed as new refining capacity comes on line. Shell, for instance, is investing US$ 7 billion in doubling the capacity of a refinery in Texas, though this will take many years to come on line.
Bio-era's numbers suggest that by 2020, given current plans, biofuels will amount to 10% of global liquid fuel use. That doesn't seem like much, but the increase from ~2% to 10% of use will account for 50% of the global increase in use, which is a big deal. I am beginning to wonder if this is already an underestimate. Many companies are making good progress in producing various liquid fuels using microbes (see previous posts here and here), and any shift away from the dollar in trading oil will cause further substitution within the U.S.
It will be interesting to see what effect this has on the economics of distributed fuel production.
CNN is reporting that methicillin-resistant Staphylococcus aureus (MRSA) is afflicting a number of high school students in the U.S. One student has died from an infection apparently contracted at school, while another 15 or so students in two states have tested positive.
This is getting press in part because of a report out in JAMA that the rate of infection from MRSA around the U.S. could be twice as high as previously thought, with a mortality rate of almost 20%. (Here is the paper on PubMed: "Invasive methicillin-resistant Staphylococcus aureus infections in the United States".) MRSA was first observed in the U.S. only in 1981. Thus over only about 25 years we have produced a bug, through profligate use of antibiotics and poor sanitation, that may be a bigger killer than even HIV.
This while NIH funding has more than doubled, where most of that money has gone to established investigators (See my post, "The Death of Innovation, or How the NIH is Undermining Its Future") doing whatever it is they do that doesn't result in new antibiotics. Where is the Health in NIH?
I heard yesterday via the grapevine that an NIH review panel failed to award any of 19 worthy new grants to younger investigators because all the money in the program is sopped up by existing grants. You could argue that we should just increase the NIH budget, to which I would be sympathetic, but it is by no means clear that the present funding is well-spent.
I spent part of last week at the "opening congress" of the Institute Para Limes (IPL) in The Netherlands. The IPL is meant to be a European version of the Santa Fe Institute (SFI) for the new century, though because of it's cultural mileau it is also meant to be something different. The meeting last week was supposed to help sort out the focus and style of the place.
Wikipedia notes that;
SFI's original mission was to disseminate the notion of a separate interdisciplinary research area, complexity theory referred to at SFI as "complexity science". Recently it has announced that its original mission to develop and disseminate a general theory of complexity has been realized. It noted that numerous complexity institutes and departments have sprung up around the world.
SFI was founded by a bunch of famous people, a Nobel Laureate included, and has been much lauded in the press, though its reputation is not universally sterling in academic circles. This is primarily because, I suspect, many people are still trying to figure out exactly what "Complexity Science" really is all about. It's a fair question. But there has been a great deal of good work done at the SFI.
The director of SFI, Geoff West, was the first speaker at the Institute Para Limes meeting, and his talk focussed both on how SFI has succeeded and also his own contributions in the areas of allometric scaling. He also spoke about this really cool paper in PNAS that I printed out last spring, but have somehow managed to not yet read, "Growth, innovation, scaling, and the pace of life in cities".
The IPL will eventually be sited in a renovated monastery in Duisberg, which is intellectually, by design, approximately in the middle of nowhere. This part of the plan for IPL confuses me a bit. It will take at least 90 minutes to get to IPL from Amsterdam, probably more if you have to change trains multiple times, like I did, and then find a taxi for the final leg. There is something to be said for making sure you have some intellectual distance from staid Universities, but in my experience it a block or two is usually enough to serve as infinitely high barriers between academic departments. At Princeton, for many years, it was an exceptionally rare sight for anyone to even cross the street between Jadwin (Physics) and Lewis Thomas (Molecular Biology) for the purposes of a scientific discussion.
The meeting was a chance for me to catch up with Sydney Brenner a bit, to stand by has he and Gerard t'Hooft got into an animated, um, communication, about the purpose of DNA, and to hear Sydney drop a few bon mots:
On "factory science" in biology: "Low input, high throughput, no output."
On evolution: "Mathematics is the art of the perfect. Physics is the art of the optimal. Biology is the art of the satisfactory. Patch it up with sticky tape, tie it up with twine, and go on. If it doesn't work, end of story, next genome."
Gerard t'Hooft had this nice bit about the process of science: "Science is about the truth. Science zooms in on the truth. The truth changes, in part due to changes in science, but the assumptions and conjectures are always periodically tested."
And Science Always Wins.
(Updated: Friday 5 Oct 19:15 PST)
A few weeks ago I heard a presentation from someone (hereafter person "A", to remain anonymous) who claimed that increasing CO2 concentrations won't cause significant global warming. The highly technical argument sounded extremely implausible to me, but it has taken me a while to sort out the details. This is worth commenting on because the argument is due to be presented in a high profile book due out next year from a very well known publisher.
I don't fault person A for falling for the "deception", but he could have been more critical given the sources he used to build up his argument.
The anti-warming argument was based on a figure from a non-peer reviewed "paper" available on the web. The figure, in turn, was generated by a fellow named David Archibald using the "modtran" model server hosted by The University of Chicago. The modtran model server is run by Professor David Archer , in the Department of Geophysical Sciences, to help his students with coursework. I wrote to Professor Archer to clarify both the intended use of the model and the interpretation of the data.
The model is evidently reasonably well accepted in its description of infrared radiation adsorption by the atmosphere as a function of CO2 concentration, otherwise known as radiative forcing. But it turns out that to estimate the resulting warming, you have to multiply the radiative forcing by the 'climate sensitivity parameter', which tells you how the atmosphere and oceans respond to added heat. The climate sensitivity parameter is actually a distribution of values, and models of climate change are usually evaluated using several different values of the parameter. David Archibald conveniently chose a value that is 40 times smaller than the most likely value in the distribution used by the IPCC. The value is in the distribution describing the climate sensitivity parameter, to be sure, but it is way the hell out to the left, and very improbable. Thus one can very accurately claim that Archibald used the correct radiative forcing numbers but he intentionally chose an estimate of climate sensitivity that nobody else believes is physically likely.
Professor Acher posted to RealClimate.org with the title, "My model, used for deception". He is relatively circumspect, though still damning, in his criticism of Archibald. The comments that follow his post, however, are ruthless. It seems I set loose the hounds.
I take the time to write this because I have become more aware of late that many climate change skeptics seem to think that anthropogenic climate change (in particular, warming caused by CO2 emissions) is simply a political ploy with no basis in physical reality. That kind of thinking denies not just climate change, but virtually all of the science our technological economy is built on. (I will certainly admit some of the rhetoric surrounding climate change bothers me, and I am not comfortable with the idea of brainwashing children to harass their parents about buying hybrid cars. See the 29 September WSJ, "Inconvenient Youths", or even the recent The Daily Show segment on absurdly over the top children's books from wingnuts on both the left and the right.)
I could care less at this point about the political side of the argument, and why people do or don't like Al Gore. Physics is physics. Science always wins. Science is self-correcting, and over the long term there ain't no politics about it. The U.S. was founded based on the enlightenment notions of tolerance and rational decision making. Alas, those words aren't in the Constitution anywhere, and they are seldom uttered inside the Beltway these days. But if we don't base our policy decisions on science, then we can just forget the U.S. as a viable economic entity, and thus as an entity capable of being the standard bearer of ideals that make this country worth living in and defending.
A couple of months ago, Drew Endy admonished me via email for using "Biobricks" as a noun. The trademark, as held by the Biobricks Foundation (BBF), describes a brand, or marque. The word "Biobricks" is an adjective describing a particular set of things conforming to a particular standard.
I finally had a chance to catch up via phone Drew yesterday, and he clarified why this is important. All the groups contributing to the MIT Registry of Standard Biological Parts, mainly via the International Genetically Engineered Machines Competition (iGEM), are working hard to make sure all those parts conform to set of rules for physical and functional assembly. That means, amongst many other requirements, that the ends of the genes have appropriate sequences for manipulation and are sequence optimized for the assembly protocols. For example, all the EcoR1 restriction enzyme sites need to be at the ends of the part and not in the middle.
It turns out that Drew is seeing lots of "parts" show up in papers and talks, described as "biobricks", that won't be compatible with the growing list of parts in the Registry refrigerators. Thus the need for a differentiable marque. From the BBF FAQ: "The BBF maintains the "biobrick(s)" trademarks in order to enable and defend the set of BioBrick™ standard biological parts as an open and free-to-use collection of standard biological parts." Thus it seems the BBF will both assert a standard and curate and license a library of parts.
There will be a BBF open workshop 4-6 November at MIT to define technical and legal standards for Biobricks Biobrick parts (it's just awkward, no?), following iGEM 2007 on 2-4 November at MIT.
Which gets me to wondering what other examples there might be of standards being defined and maintained by a foundation, protected with a trademark. As far as I know, "transistor-transistor logic" (TTL) became a standard simply because Texas Instruments put a bunch of products out and everybody else jumped on board (see Wikipedia). But nobody protected the marque "TTL", and no one organization curated and licensed a library of TTL parts. Similarly, if I have got this right, the IEEE discusses and approves standards for hardware and software that manufacturers and programmers can use, but the IEEE does not itself play a role in building or licensing anything. (Comments? Randy? TK?)
So I wonder if the BBF isn't heading out into some unknown territory. Obviously, the idea of Biobricks Biobrick parts (Argh!) is itself new and interesting, but I wonder what the effect on innovation will be under an apparently new kind of IP regime if one organization is in a position to "defend" not just a a standard but also parts that conform to the standard. What happens if the leadership (or control) of the BBF changes and suddenly the "open and free-to-use collection" becomes not so open? And am I free to build/identify a new part as a Biobrick part (!) without submitting it to the Registry or the BBF? Can I even advertise something as being compatible with the standard on my own, or do I have to have permission from the BBF to even suggest in public that I have something other people might want to use/buy that works with all the other Biobrick™ parts? And who exactly controls the Registry? (The "About the Registry" page doesn't appear to answer this question, even though I believe I have heard Drew and Randy Rettburg say in the past that MIT presently controls the IP. There was also, I believe, some question as to whether some parts in the Registry are actually owned by other organizations.)
So many questions. It is clear that there is lot's of work to do...
ScienceDaily has a story describing a new paper showing that the rate of protein evolution is subject to allometric scaling. Actually, now that I have written that, I remember that allometric scaling describes a specfic mathematical relationship between metabolism and body mass, but the paper in question doesn't appear to be online yet so I can't say for sure allometric scaling is the appropriate mechanism to cite.
At any rate, ScienceDaily reports that James Gillooly, and colleagues have shown that: "...A 10-degree increase in temperature across species leads to about a 300 percent increase in the evolutionary rate of proteins, while a tenfold decrease in body size leads to about a 200 percent increase in evolutionary rates."
"Generally, there are two schools of thought about what affects evolution," said Andrew P. Allen, Ph.D., a researcher with the National Center for Ecological Analysis and Synthesis in Santa Barbara, Calif. "One says the environment dictates changes that occur in the genome and phenotype of a species, and the other says the DNA mutation rate drives these changes. Our findings suggest physiological processes that drive mutation rates are important."
That is pretty interesting. Warm, small animals evidently experience a greater rate of protein evolution than to large, cold ones. This suggests to me that warm-blooded, smaller animals have an evolutionary advantage because they are better able to produce physiological variation in the context of a changing environment, and thus better able to compete at the species level in the face of natural selection. The ScienceDaily story doesn't make that point, but I would assume the paper in Biology Letters, when it is published, will.
Here is the press release from the University of Florida.
The HTML version of my 2000 essay from the Shell/Economist Writing Competition seems to have fallen off the web. Here is another copy: "Biological Technology in 2050".
Amyris Biotechnologies today announced the first portion of their B round financing for US$ 70 million. This brings the total company financing for microbial production of biofuels to just under US$ 100 million in the last year. The press release also notes Amyris already has bugs in the lab producing "bio-jet", "bio-diesel", and "bio-gasoline". The latter is interesting because previous announcements had suggested butanol as a target product rather than a hydrocarbon. Immiscible hydrocarbons will be much easier (read "less expensive") to separate from the fermentation broth than water soluble alcohols.
In any event, the company is clearly moving faster than even my earlier optimistic estimates (see "The Need for Fuels Produced Using Synthetic Biology"). While the speed of engineering efforts is still an issue (see "The Intersection of Biofuels and Synthetic Biology"), and will be for some time to come, I have been spending more time lately trying to understand the issue of scale. The petroleum industry is absolutely enormous, and replacing any significant amount of petro-fuels with bio-fuels will require feedstocks in abundance. It is by no means clear that the U.S. can meet the demand with domestic biomass production. More on this as the topic develops.